Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix what looks like a bug in FlowBasedRead #8576

Closed
wants to merge 1 commit into from
Closed
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
public static final int MAX_CLASS = 12; //note - this is a historical value to support files with max class is not defined in the header, it is expected that mc tag exists in the CRAM
public static final String DEFAULT_FLOW_ORDER = "TGCA";
private static final long serialVersionUID = 42L;
private final Logger logger = LogManager.getLogger(this.getClass());
private static final Logger logger = LogManager.getLogger(FlowBasedRead.class);

Check warning on line 44 in src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java

View check run for this annotation

Codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java#L44

Added line #L44 was not covered by tests
private static final OneShotLogger vestigialOneShotLogger = new OneShotLogger(FlowBasedRead.class);

// constants
Expand Down Expand Up @@ -433,6 +433,7 @@
for (final int b : key) {
if (b > maxHmer - 1) {
validKey = false;
return;

Check warning on line 436 in src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java

View check run for this annotation

Codecov / codecov/patch

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java#L436

Added line #L436 was not covered by tests
}
}
validKey = true;
Expand Down
Loading